UCEs are depleted from pooled de nov°CNVs, enriched in pooled cancerCNAs, and depleted from pooled somaticCNVs and high passage iPSCNVs.

Here, we show the relationship between 896 HMR-HDM-HC UCEs and de nov°CNVs, cancerCNAs, somaticCNVs, and iPSCNVs, reporting the results for pooled datasets as well as all individual datasets that met our requirement for 20 Mb of coverage (Table S3). Individual CNV and CNA datasets are named according to the first author and the year of the study.aThe pooled de nov°CNV dataset included datasets from Xu 2008 [69], Itsara 2010 [70], Malhotra 2011 [71], and Sanders 2011 [72], which were too small to be considered on their own.bThe pooled cancerCNA dataset included all the cancerCNA datasets listed in this table, except for Walker 2012 [87], which was excluded to avoid bias from its extensive coverage of the genome, and also included the datasets Bullinger 2010 [78], Nik-Zainal 2012 [85], Holmfeldt 2013 [89], and Weischenfeldt 2013 [91], which were too small to be considered on their own.cThe pooled somaticCNV dataset included the four somaticCNV datasets listed in this table as well as Piotrowski 2008 [63] and O'Huallachain 2012 [67], which were too small to be considered on their own.dThe pooled iPSCNV datasets were comprised of CNVs from low, medium, and high passage iPS cells from the two datasets Hussein 2011 [100] and Laurent 2011 [98]. Proportion, P-value, and obs/exp, as described for Table 1. Outcome: determined with a one-tailed test (α = 0.05) for the pooled de nov°CNV dataset because dataset was analyzed prior to our discovery that CNVs can be enriched for UCEs; all other assessments of depletion or enrichment carried out with a two-tailed test (P≤0.025 in each tail for an overall α of 0.05). NA (not applicable): expected overlaps not normally distributed, precluding a Z-test.UCEs are depleted from pooled de nov°CNVs, enriched in pooled cancerCNAs, and depleted from pooled somaticCNVs and high passage iPSCNVs.